diff --git a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
index 59599880602fb9d38b6741ae242966066ecd787f..56823222d6625ab0ba7ef8c27bbb8a472fad3a05 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
@@ -15,7 +15,10 @@ import java.util.Map;
*/
public final class TextFileUtils {
- public static String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
+ /**
+ * Name of the param that contains number of columns.
+ */
+ public static final String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
/**
* Default constructor that prevents instatiation.
diff --git a/frontend-js/package.json b/frontend-js/package.json
index 6f5aec9080ff4d2fb572ce57121c7cfef6f0c418..fdaa210ba8bad3b808b9f23c471706a27aa17f46 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -4,9 +4,13 @@
"description": "frontentd for minerva google maps interface",
"main": "minerva.js",
"scripts": {
- "build": "rm -rf dist & rmdir /q /s dist & mkdir dist & browserify --debug --standalone minerva src/main/js/minerva.js | exorcist dist/minerva.js.map > dist/minerva.js ",
+ "build:css": "cleancss -o dist/minerva.css node_modules/dual-listbox/dist/*.css src/main/css/*.css",
+ "build:js": "browserify --debug --standalone minerva src/main/js/minerva.js | exorcist dist/minerva.js.map > dist/minerva.js ",
"//": "rm -rf dist & rmdir /q /s dist & mkdir dist & browserify --debug --standalone minerva src/main/js/minerva.js | exorcist dist/minerva.js.map > dist/minerva.js & uglifyjs --compress --mangle --in-source-map dist/minerva.js.map --source-map-include-sources --source-map dist/minerva.min.js.map -o dist/minerva.min.js dist/minerva.js",
- "build-deploy": "rm -rf dist & rmdir /q /s dist & mkdir dist & browserify --debug --standalone minerva src/main/js/minerva.js | exorcist dist/minerva.js.map > dist/minerva.js & copy /Y \"dist\\*\" \"C:/Program Files/apache-tomcat-7.0.72/webapps/minerva/resources/js\" ",
+ "build-deploy": "npm run build && npm run deploy",
+ "build": "npm run clean && npm run build:css && npm run build:js",
+ "clean": "rm -rf dist & rmdir /q /s dist & mkdir dist",
+ "deploy": "copy /Y \"dist\\*.js*\" \"C:/Program Files/apache-tomcat-7.0.72/webapps/minerva/resources/js\" && copy /Y \"dist\\*.css\" \"C:/Program Files/apache-tomcat-7.0.72/webapps/minerva/resources/css\" ",
"lint": "jshint src/.",
"test": "istanbul cover node_modules/mocha/bin/_mocha -- --recursive src/test/js"
},
@@ -17,13 +21,14 @@
"bootstrap": "^3.3.7",
"browserify": "^13.1.1",
"chai": "^3.5.0",
+ "clean-css-cli": "^4.1.6",
"datatables.net": "^1.10.13",
"exorcist": "^0.4.0",
"file-url": "^2.0.0",
"istanbul": "0.4.5",
"jquery": "3.1.1",
"jquery-ui-dist": "^1.12.1",
- "jsdom": "^9.9.1",
+ "jsdom": "^11.1.0",
"jsdom-global": "^2.1.1",
"jshint": "^2.9.4",
"log4js-memory-appender": "1.0.5",
@@ -31,6 +36,7 @@
"uglifyjs": "^2.4.10"
},
"dependencies": {
+ "dual-listbox": "^1.0.3",
"http-status-codes": "^1.1.6",
"js-cookie": "^2.1.3",
"log4js": "0.6.38",
diff --git a/web/src/main/webapp/resources/css/global.css b/frontend-js/src/main/css/global.css
similarity index 82%
rename from web/src/main/webapp/resources/css/global.css
rename to frontend-js/src/main/css/global.css
index bf9f50b07e8c6803597a6cf5e9dfe9ab47a2f6d8..da6f6288d13d1ecb9948cdb7a16e460282b43f28 100644
--- a/web/src/main/webapp/resources/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -34,6 +34,23 @@ table.mapInfoBoxResultsTable, table.mapInfoBoxResultsTable th, table.mapInfoBoxR
transition: background-color 0.4s ease-in-out 0s;
}
+.minerva-checkbox-grid li {
+ display: block;
+ float: left;
+ width: 20%;
+}
+
+.minerva-checkbox-grid li .checkbox {
+ margin-top: 2px;
+ margin-bottom: 2px;
+}
+
+.minerva-checkbox-grid:after {
+ content: '';
+ display: block;
+ clear: both;
+}
+
.mapChartNameDiv {
width: 150px;
float: left;
@@ -325,4 +342,39 @@ table.mapInfoBoxResultsTable, table.mapInfoBoxResultsTable th, table.mapInfoBoxR
-webkit-border-radius: 6px 0 6px 6px;
-moz-border-radius: 6px 0 6px 6px;
border-radius: 6px 0 6px 6px;
+}
+
+.dual-listbox .dual-listbox__search {
+ display: none;
+}
+
+.dual-listbox .dual-listbox__title {
+ padding: 5px 2px;
+}
+
+.dual-listbox .dual-listbox__item {
+ padding: 2px;
+}
+
+.dual-listbox .dual-listbox__button {
+ background-color: #999;
+}
+
+.minerva-multi-select-special {
+ background-color: #00FF00;
+}
+
+.dual-listbox__item--selected .minerva-multi-select-special {
+ background-color: rgba(8, 157, 227, .7);
+}
+
+.dual-listbox .dual-listbox__available, .dual-listbox .dual-listbox__selected
+ {
+ width: 200px;
+ height: 200px;
+}
+
+.minerva-export-dual-listbox-container {
+ padding: 10px;
+ float: left;
}
\ No newline at end of file
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index 7932fc1ad7870d0bb0f106f34bce21fb0af29877..9fbbb38b0aa1a24799fe39331090574e76dfbfb2 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -5,6 +5,7 @@
var logger = require('./logger');
var ConfigurationType = require('./ConfigurationType');
+var MiriamType = require('./map/data/MiriamType');
function Configuration(json) {
var self = this;
@@ -44,6 +45,7 @@ function Configuration(json) {
self.setModelConverters(json.modelFormats);
self.setElementTypes(json.elementTypes);
self.setReactionTypes(json.reactionTypes);
+ self.setMiriamTypes(json.miriamTypes);
}
Configuration.prototype.setOption = function(type, value) {
@@ -88,4 +90,24 @@ Configuration.prototype.getReactionTypes = function() {
return this._reactionTypes;
};
+Configuration.prototype.setMiriamTypes = function(miriamTypes) {
+ this._miriamTypes = [];
+ for ( var key in miriamTypes) {
+ if (miriamTypes.hasOwnProperty(key)) {
+ var typeData = miriamTypes[key];
+ this._miriamTypes.push(new MiriamType(typeData, key));
+ }
+ }
+};
+Configuration.prototype.getMiriamTypeByName = function(name) {
+ var self = this;
+ for (var i = 0; i < self._miriamTypes.length; i++) {
+ var miriamType = self._miriamTypes[i];
+ if (miriamType.getName() === name) {
+ return miriamType;
+ }
+ }
+ return null;
+};
+
module.exports = Configuration;
diff --git a/frontend-js/src/main/js/Export.js b/frontend-js/src/main/js/Export.js
new file mode 100644
index 0000000000000000000000000000000000000000..265a6fc52fb79509e759ad0b14fe0f71ba02bde2
--- /dev/null
+++ b/frontend-js/src/main/js/Export.js
@@ -0,0 +1,156 @@
+"use strict";
+
+var Promise = require("bluebird");
+
+var CustomMapOptions = require('./map/CustomMapOptions');
+var ElementExportPanel = require('./gui/export/ElementExportPanel');
+var GraphicsExportPanel = require('./gui/export/GraphicsExportPanel');
+var NetworkExportPanel = require('./gui/export/NetworkExportPanel');
+var Header = require('./gui/Header');
+var ObjectWithListeners = require('./ObjectWithListeners');
+
+var logger = require('./logger');
+var Functions = require('./Functions');
+
+/**
+ * Default constructor.
+ *
+ * @param options
+ * CustomMapOptions object representing all parameters needed for map
+ * creation
+ */
+function Export(options) {
+ var self = this;
+ self._panels = [];
+ if (!(options instanceof CustomMapOptions)) {
+ options = new CustomMapOptions(options);
+ }
+ self.setProject(options.getProject());
+ self.setElement(options.getElement());
+
+ self._createGui();
+}
+
+Export.prototype = Object.create(ObjectWithListeners.prototype);
+Export.prototype.constructor = ObjectWithListeners;
+
+Export.prototype._createGui = function() {
+ var self = this;
+ self.getElement().innerHTML = "";
+ var headerDiv = Functions.createElement({
+ type : "div"
+ });
+ new Header({
+ element : headerDiv,
+ customMap : null,
+ project : self.getProject(),
+ });
+ self.getElement().appendChild(headerDiv);
+
+ var panels = [ {
+ name : "ELEMENTS",
+ panelClass : ElementExportPanel,
+ }, {
+ name : "NETWORK",
+ panelClass : NetworkExportPanel,
+ }, {
+ name : "GRAPHICS",
+ panelClass : GraphicsExportPanel,
+ } ];
+
+ var tabDiv = Functions.createElement({
+ type : "div",
+ name : "tabView",
+ className : "tabbable boxed parentTabs"
+ });
+ self.getElement().appendChild(tabDiv);
+
+ var tabMenuDiv = Functions.createElement({
+ type : "ul",
+ className : "nav nav-tabs"
+ });
+ tabDiv.appendChild(tabMenuDiv);
+
+ var tabContentDiv = Functions.createElement({
+ type : "div",
+ className : "tab-content"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ for (var i = 0; i < panels.length; i++) {
+ self.addTab(panels[i], tabMenuDiv, tabContentDiv);
+ }
+
+}
+
+Export.prototype.addTab = function(params, navElement, contentElement) {
+ var self = this;
+
+ var name = params.name;
+
+ var tabId = "left_panel_ab_" + this._tabIdCount;
+ self._tabIdCount++;
+
+ var navClass = '';
+ var contentClass = 'tab-pane';
+ if (navElement.children.length === 0) {
+ navClass = "active";
+ contentClass = "tab-pane active";
+ }
+
+ var navLi = document.createElement("li");
+ navLi.className = navClass;
+
+ var navLink = document.createElement("a");
+ navLink.href = "#" + tabId;
+ if (name !== undefined) {
+ if (name.length > 12) {
+ name = name.substring(0, 10) + "...";
+ }
+ navLink.innerHTML = name;
+ }
+ navLink.onclick = function() {
+ $(this).tab('show');
+ };
+ navLi.appendChild(navLink);
+ if (name !== undefined) {
+ navLink.innerHTML = name;
+ }
+ navElement.appendChild(navLi);
+
+ var contentDiv = document.createElement("div");
+ contentDiv.style.height = "100%";
+ contentDiv.className = contentClass;
+ contentDiv.id = tabId;
+
+ contentElement.appendChild(contentDiv);
+
+ this._panels.push(new params.panelClass({
+ element : contentDiv,
+ project : self.getProject(),
+ }));
+};
+
+Export.prototype.setProject = function(project) {
+ this._project = project;
+};
+Export.prototype.getProject = function() {
+ return this._project;
+};
+
+Export.prototype.setElement = function(element) {
+ this._element = element;
+};
+Export.prototype.getElement = function() {
+ return this._element;
+};
+
+Export.prototype.init = function() {
+ var promises = [];
+ for (var i = 0; i < this._panels.length; i++) {
+ promises.push(this._panels[i].init());
+ }
+ return Promise.all(promises);
+};
+
+module.exports = Export;
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index b7f9cb0028505d75a4423dcbc750d8de93701afc..a12a922ce8834f4d06e74adb9de0a6f3340cdfd9 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -24,6 +24,7 @@ var LayoutReaction = require('./map/data/LayoutReaction');
var MiRna = require('./map/data/MiRna');
var NetworkError = require('./NetworkError');
var Project = require('./map/data/Project');
+var ProjectStatistics = require('./map/data/ProjectStatistics');
var Reaction = require('./map/data/Reaction');
var ReferenceGenome = require('./map/data/ReferenceGenome');
var SecurityError = require('./SecurityError');
@@ -323,6 +324,13 @@ ServerConnector.getProjectsUrl = function(queryParams, filterParams) {
});
};
+ServerConnector.getProjectStatisticsUrl = function(queryParams, filterParams) {
+ return this.getApiUrl({
+ url : this.getProjectsUrl(queryParams) + "statistics/",
+ params : filterParams,
+ });
+};
+
ServerConnector.getPublicationsUrl = function(queryParams, filterParams) {
filterParams.start = filterParams.start || 0;
filterParams.length = filterParams.length || 10;
@@ -628,6 +636,22 @@ ServerConnector.getProject = function(projectId) {
});
};
+ServerConnector.getProjectStatistics = function(projectId) {
+ var queryParams = {};
+ var filterParams = {};
+ var self = this;
+ var content;
+ return self.getProjectId(projectId).then(function(result) {
+ queryParams.projectId = result;
+ return self.readFile(self.getProjectStatisticsUrl(queryParams, filterParams));
+ }).then(function(result) {
+ content = JSON.parse(result);
+ return self.getConfiguration();
+ }).then(function(configuration) {
+ return new ProjectStatistics(content, configuration);
+ });
+};
+
ServerConnector.getLoggedUser = function() {
var self = this;
if (self._loggedUser !== undefined) {
@@ -788,14 +812,20 @@ ServerConnector.getReactions = function(params) {
});
};
-ServerConnector.getAliases = function(aliasIds, projectId, columns) {
+ServerConnector.getAliases = function(params) {
var self = this;
- var queryParams = {};
+ var queryParams = {
+ modelId : params.modelId,
+ };
+ if (params.ids === undefined) {
+ params.ids = []
+ }
var filterParams = {
- id : aliasIds,
- columns : columns
+ id : params.ids,
+ columns : params.columns,
+ type : params.type,
};
- return self.getProjectId(projectId).then(function(result) {
+ return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
if (filterParams.id.length > 100) {
return self.sendPostRequest(self.getAliasesUrl(queryParams), filterParams);
@@ -840,10 +870,6 @@ ServerConnector.getComments = function(params) {
});
};
-ServerConnector.getLightAliases = function(aliasIds, projectId) {
- return this.getAliases(aliasIds, projectId, "id,bounds,modelId");
-};
-
ServerConnector.getSessionData = function(project) {
if (this._sessionData === undefined) {
this._sessionData = new SessionData(project);
diff --git a/frontend-js/src/main/js/gui/AbstractGuiElement.js b/frontend-js/src/main/js/gui/AbstractGuiElement.js
index ee43bfa234ab841567c8941fcc89259d4a307c3e..4612ed9afe9d04a865f8e44403c10362f70910bd 100644
--- a/frontend-js/src/main/js/gui/AbstractGuiElement.js
+++ b/frontend-js/src/main/js/gui/AbstractGuiElement.js
@@ -13,6 +13,7 @@ function AbstractGuiElement(params) {
var self = this;
self.setElement(params.element);
+ self.setProject(params.project);
self.setConfiguration(params.configuration);
self.setMap(params.customMap);
@@ -24,7 +25,7 @@ AbstractGuiElement.prototype = Object.create(ObjectWithListeners.prototype);
AbstractGuiElement.prototype.constructor = AbstractGuiElement;
AbstractGuiElement.prototype.setMap = function(map) {
- if (map === undefined || map === null) {
+ if (map === undefined) {
throw new Error("map must be defined");
}
this._map = map;
@@ -53,6 +54,18 @@ AbstractGuiElement.prototype.getConfiguration = function() {
return this._configuration;
};
+AbstractGuiElement.prototype.setProject = function(project) {
+ this._project = project;
+};
+
+AbstractGuiElement.prototype.getProject = function() {
+ if (this._project === undefined || this._project === null) {
+ return this.getMap().getProject();
+ } else {
+ return this._project;
+ }
+};
+
AbstractGuiElement.prototype.setControlElement = function(type, element) {
if (type === null || type === undefined) {
throw new Error("Unknown controle element type");
diff --git a/frontend-js/src/main/js/gui/Header.js b/frontend-js/src/main/js/gui/Header.js
index cf0cb27fe4d56f7962c376782d545e9a6aa391c0..cd078fcc8ca83c5fb475384fa73eab36b6af87b5 100644
--- a/frontend-js/src/main/js/gui/Header.js
+++ b/frontend-js/src/main/js/gui/Header.js
@@ -24,8 +24,8 @@ Header.prototype._createHeaderGui = function() {
var self = this;
self.getElement().className = "minerva-header";
- var projectId = self.getMap().getProject().getProjectId();
- var projectName = self.getMap().getProject().getName();
+ var projectId = self.getProject().getProjectId();
+ var projectName = self.getProject().getName();
var loadingDiv = Functions.createElement({
type : "div",
diff --git a/frontend-js/src/main/js/gui/leftPanel/Panel.js b/frontend-js/src/main/js/gui/Panel.js
similarity index 92%
rename from frontend-js/src/main/js/gui/leftPanel/Panel.js
rename to frontend-js/src/main/js/gui/Panel.js
index 5abbe4131e045ff1c09739453ffcb3123104062d..c8fb548235b86083d00619189a94ece2ff5cb50d 100644
--- a/frontend-js/src/main/js/gui/leftPanel/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -2,13 +2,13 @@
/* exported logger */
-var GuiConnector = require('../../GuiConnector');
-var AbstractGuiElement = require('../AbstractGuiElement');
-var GuiUtils = require('./GuiUtils');
-var PanelControlElementType = require('../PanelControlElementType');
-var Functions = require('../../Functions');
+var GuiConnector = require('../GuiConnector');
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiUtils = require('./leftPanel/GuiUtils');
+var PanelControlElementType = require('./PanelControlElementType');
+var Functions = require('../Functions');
-var logger = require('../../logger');
+var logger = require('../logger');
function Panel(params) {
AbstractGuiElement.call(this, params);
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
new file mode 100644
index 0000000000000000000000000000000000000000..737b49cbfaeb8d318faa043f471429c1e8b21462
--- /dev/null
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -0,0 +1,598 @@
+"use strict";
+
+/* exported logger */
+
+var Panel = require('../Panel');
+
+var DualListbox = require('dual-listbox').DualListbox;
+var GuiConnector = require('../../GuiConnector');
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+var Promise = require("bluebird");
+
+function ElementExportPanel(params) {
+ params.panelName = "elementExport";
+ params.scrollable = true;
+ Panel.call(this, params);
+
+ var self = this;
+ self._createGui();
+}
+
+ElementExportPanel.prototype = Object.create(Panel.prototype);
+ElementExportPanel.prototype.constructor = ElementExportPanel;
+
+function compareSimple(val1, val2) {
+ if (val1 < val2)
+ return -1;
+ if (val1 > val2)
+ return 1;
+ return 0;
+}
+
+ElementExportPanel.prototype._createGui = function() {
+
+};
+
+ElementExportPanel.prototype.init = function() {
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ return ServerConnector.getConfiguration().then(function(result) {
+ configuration = result;
+ var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
+ element.appendChild(typeDiv);
+ element.appendChild(self._createSelectColumnDiv());
+ return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
+ }).then(function(statistics) {
+ var miriamDiv = self._createMiriamTypeDiv(statistics);
+ element.appendChild(miriamDiv);
+ self.setMiriamTypesDualListbox(new DualListbox("#miriamTypeSelect", {
+ availableTitle : 'Available',
+ selectedTitle : 'Used',
+ addButtonText : '>',
+ removeButtonText : '<',
+ addAllButtonText : '>>',
+ removeAllButtonText : '<<'
+ }));
+ }).then(function() {
+ return self._createSelectIncludedCompartmentDiv();
+ }).then(function(selectIncludedCompartmentDiv) {
+ element.appendChild(selectIncludedCompartmentDiv);
+ self.setIncludedCompartmentsDualListbox(new DualListbox("#includedCompartmentsSelect", {
+ availableTitle : 'Available',
+ selectedTitle : 'Used',
+ addButtonText : '>',
+ removeButtonText : '<',
+ addAllButtonText : '>>',
+ removeAllButtonText : '<<'
+ }));
+ return self._createSelectExcludedCompartmentDiv();
+ }).then(function(selectExcludedCompartmentDiv) {
+ element.appendChild(selectExcludedCompartmentDiv);
+ self.setExcludedCompartmentsDualListbox(new DualListbox("#excludedCompartmentsSelect", {
+ availableTitle : 'Available',
+ selectedTitle : 'Used',
+ addButtonText : '>',
+ removeButtonText : '<',
+ addAllButtonText : '>>',
+ removeAllButtonText : '<<'
+ }));
+ element.appendChild(self._createDownloadButton());
+ }).then(function() {
+ $(window).trigger('resize');
+ });
+}
+
+ElementExportPanel.prototype._createSelectTypeDiv = function(elementTypes) {
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "typeSelectDiv",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " TYPE:",
+ }));
+ var choicesContainer = Functions.createElement({
+ type : "ul",
+ className : "minerva-checkbox-grid"
+ });
+ typeDiv.appendChild(choicesContainer);
+ for (var i = 0; i < elementTypes.length; i++) {
+ var elementType = elementTypes[i];
+ var row = Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + elementType + "\" value=\""
+ + elementType + "\" />" + elementType + "</label></div>"
+ });
+ choicesContainer.appendChild(row);
+ }
+ choicesContainer.appendChild(Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
+ }));
+ return typeDiv;
+}
+
+ElementExportPanel.prototype._createMiriamTypeDiv = function(statistics) {
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "miriamSelectDiv",
+ className : "minerva-export-dual-listbox-container",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " Annotations:",
+ }));
+
+ var annotations = statistics.getElementAnnotations();
+
+ var selectElement = Functions.createElement({
+ type : "select",
+ className : "minerva-multi-select",
+ id : "miriamTypeSelect",
+ });
+ typeDiv.appendChild(selectElement);
+
+ function compare(entry1, entry2) {
+ var result;
+ if ((entry1.count === 0 && entry2.count === 0) || (entry1.count !== 0 && entry2.count !== 0))
+ return compareSimple(entry1.miriamType.getCommonName(), entry2.miriamType.getCommonName());
+ else {
+ return compareSimple(-entry1.count, -entry2.count);
+ }
+ }
+ annotations.sort(compare);
+
+ for (var i = 0; i < annotations.length; i++) {
+ var miriamType = annotations[i].miriamType;
+ var count = annotations[i].count;
+
+ var option = new Option();
+ option.value = miriamType.getName();
+ if (count > 0) {
+ option.innerHTML = "<div class='minerva-multi-select-special'>" + miriamType.getCommonName() + " (" + count
+ + ")</div>";
+ } else {
+ option.innerHTML = "<div >" + miriamType.getCommonName() + "</div>";
+ }
+ selectElement.appendChild(option);
+ }
+ return typeDiv;
+};
+
+ElementExportPanel.prototype._createDownloadButton = function() {
+ var self = this;
+ var downloadDiv = Functions.createElement({
+ type : "div",
+ name : "downloadDiv",
+ style : "clear:both; padding: 10px;",
+ });
+ var button = Functions.createElement({
+ type : "button",
+ content : " Download",
+ onclick : function() {
+ return self.createResponseString().then(function(result) {
+ logger.info(result);
+ });
+ },
+ })
+ downloadDiv.appendChild(button);
+
+ return downloadDiv;
+};
+
+ElementExportPanel.prototype.createResponseString = function() {
+ var self = this;
+ var types;
+ var includedCompartmentsName;
+ var models = [ self.getProject().getModel() ];
+ for (var i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
+ models.push(self.getProject().getModel().getSubmodels()[i]);
+ }
+
+ var elements = [];
+ return self.getSelectedTypes().then(function(result) {
+ types = result;
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getAliases({
+ type : types,
+ complete : true,
+ }));
+ }
+ return Promise.all(promises);
+ }).then(function(aliasesByModel) {
+ for (var i = 0; i < aliasesByModel.length; i++) {
+ for (var j = 0; j < aliasesByModel[i].length; j++) {
+ elements.push(aliasesByModel[i][j]);
+ }
+ }
+ return self.getSelectedColumns();
+ }).then(function(selectedColumns) {
+
+ var rows = [];
+ rows.push(self.createResponseHeader(selectedColumns));
+ for (var i = 0; i < elements.length; i++) {
+ rows.push(self.createResponseRow(elements[i], selectedColumns));
+ }
+ return rows.join("\n");
+ });
+};
+
+ElementExportPanel.prototype.createResponseHeader = function(columns) {
+ var stringBuilder = [];
+ for (var i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ stringBuilder.push(column.name);
+ }
+ var result = stringBuilder.join("\t");
+ return result;
+
+};
+
+ElementExportPanel.prototype.createResponseRow = function(alias, columns) {
+ var stringBuilder = [];
+ for (var i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ var value = alias[column.method]();
+ if (column.formatFunction !== undefined) {
+ value = column.formatFunction(value);
+ }
+ stringBuilder.push(value);
+
+ }
+ var result = stringBuilder.join("\t");
+ return result;
+};
+
+ElementExportPanel.prototype._createSelectIncludedCompartmentDiv = function() {
+ var i = 0;
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "includedCompartmentSelectDiv",
+ className : "minerva-export-dual-listbox-container",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " Included compartment/pathways:",
+ }));
+
+ return self._getCompartmentNames().then(function(compartmentNames) {
+
+ var selectElement = Functions.createElement({
+ type : "select",
+ className : "minerva-multi-select",
+ id : "includedCompartmentsSelect",
+ });
+ typeDiv.appendChild(selectElement);
+
+ for (var i = 0; i < compartmentNames.length; i++) {
+ var name = compartmentNames[i];
+
+ var option = new Option();
+ option.value = name;
+ option.innerHTML = "<div >" + name + "</div>";
+ selectElement.appendChild(option);
+ }
+ return typeDiv;
+ });
+};
+
+ElementExportPanel.prototype._createSelectExcludedCompartmentDiv = function() {
+ var i = 0;
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type : "div",
+ name : "excludedCompartmentSelectDiv",
+ className : "minerva-export-dual-listbox-container",
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " Excluded compartment/pathways:",
+ }));
+
+ return self._getCompartmentNames().then(function(compartmentNames) {
+
+ var selectElement = Functions.createElement({
+ type : "select",
+ className : "minerva-multi-select",
+ id : "excludedCompartmentsSelect",
+ });
+ typeDiv.appendChild(selectElement);
+
+ for (var i = 0; i < compartmentNames.length; i++) {
+ var name = compartmentNames[i];
+
+ var option = new Option();
+ option.value = name;
+ option.innerHTML = "<div >" + name + "</div>";
+ selectElement.appendChild(option);
+ }
+ return typeDiv;
+ });
+};
+
+ElementExportPanel.prototype._getAllCompartments = function() {
+ var self = this;
+ var compartments = [];
+ var i;
+
+ var models = [ self.getProject().getModel() ];
+ for (i = 0; i < self.getProject().getModel().getSubmodels().length; i++) {
+ models.push(self.getProject().getModel().getSubmodels()[i]);
+ }
+
+ var promises = [];
+ for (i = 0; i < models.length; i++) {
+ promises.push(models[i].getCompartments());
+ }
+
+ return Promise.all(promises).then(function(result) {
+ for (var i = 0; i < result.length; i++) {
+ var modelCompartments = result[i];
+ for (var j = 0; j < modelCompartments.length; j++) {
+ compartments.push(modelCompartments[j]);
+ }
+ }
+ return compartments;
+ });
+};
+ElementExportPanel.prototype._getCompartmentNames = function() {
+ var self = this;
+ var compartments = [];
+ var i;
+ return self._getAllCompartments().then(function(result) {
+
+ var addedNames = [];
+ for (var i = 0; i < result.length; i++) {
+ if (addedNames[result[i].getName()] === undefined) {
+ compartments.push(result[i].getName());
+ addedNames[result[i].getName()] = true;
+ }
+ }
+ compartments.sort(compareSimple);
+ return compartments;
+ });
+};
+
+ElementExportPanel.prototype._createSelectColumnDiv = function() {
+ var self = this;
+ var columnDiv = Functions.createElement({
+ type : "div",
+ name : "columnSelectDiv",
+ });
+ columnDiv.appendChild(Functions.createElement({
+ type : "h4",
+ content : " COLUMN:",
+ }));
+ var choicesContainer = Functions.createElement({
+ type : "ul",
+ className : "minerva-checkbox-grid"
+ });
+ var columnTypes = self.getAllColumns();
+
+ columnDiv.appendChild(choicesContainer);
+ for (var i = 0; i < columnTypes.length; i++) {
+ var columnType = columnTypes[i];
+ var row = Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
+ + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>"
+ });
+ choicesContainer.appendChild(row);
+ }
+ choicesContainer.appendChild(Functions.createElement({
+ type : "li",
+ content : "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>"
+ }));
+ return columnDiv;
+}
+
+ElementExportPanel.prototype.getAllColumns = function() {
+ return [ {
+ "columnName" : "id",
+ "method" : "getId",
+ "name" : "Id",
+ }, {
+ "columnName" : "name",
+ "method" : "getName",
+ "name" : "Name",
+ }, {
+ "columnName" : "description",
+ "method" : "getDescription",
+ "name" : "Description",
+ }, {
+ "columnName" : "modelId",
+ "method" : "getModelId",
+ "name" : "Model",
+ }, {
+ "columnName" : "type",
+ "method" : "getType",
+ "name" : "Type",
+ }, {
+ "columnName" : "complexId",
+ "method" : "getComplexId",
+ "name" : "Complex",
+ }, {
+ "columnName" : "compartmentId",
+ "method" : "getCompartmentId",
+ "name" : "Compartment",
+ }, {
+ "columnName" : "charge",
+ "method" : "getCharge",
+ "name" : "Charge",
+ }, {
+ "columnName" : "symbol",
+ "method" : "getSymbol",
+ "name" : "Symbol",
+ }, {
+ "columnName" : "fullName",
+ "method" : "getFullName",
+ "name" : "Full name",
+ }, {
+ "columnName" : "abbreviation",
+ "method" : "getAbbreviation",
+ "name" : "Abbreviation",
+ }, {
+ "columnName" : "formula",
+ "method" : "getFormula",
+ "name" : "Formula",
+ }, {
+ "columnName" : "synonyms",
+ "method" : "getSynonyms",
+ "name" : "Synonyms",
+ }, {
+ "columnName" : "formerSymbols",
+ "method" : "getFormerSymbols",
+ "name" : "Former symbols",
+ }, {
+ "columnName" : "references",
+ "method" : "getReferences",
+ "name" : "References",
+ "formatFunction" : function(references) {
+ var stringBuilder = [];
+ for (var i = 0; i < references.length; i++) {
+ var reference = references[i];
+ stringBuilder.push(reference.getType() + ":" + reference.getResource());
+ }
+ return stringBuilder.join(",");
+ },
+ }, {
+ "columnName" : "linkedSubmodelId",
+ "method" : "getLinkedSubmodelId",
+ "name" : "Linked submodel",
+ }, {
+ "columnName" : "elementId",
+ "method" : "getElementId",
+ "name" : "Element external id",
+ }, ];
+};
+
+ElementExportPanel.prototype.getSelectedTypes = function() {
+ var self = this;
+
+ var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
+ var result = [];
+ var selectedAll = false
+ $(":checked", $(div)).each(function(index, element) {
+ if (element.value === "ALL") {
+ selectedAll = true;
+ }
+ result.push(element.value);
+ });
+ if (selectedAll) {
+ return ServerConnector.getConfiguration().then(function(configuration) {
+ return configuration.getElementTypes();
+ });
+ }
+
+ return Promise.resolve(result);
+}
+
+ElementExportPanel.prototype.setMiriamTypesDualListbox = function(dualListbox) {
+ this._miriamTypesDualListbox = dualListbox;
+};
+ElementExportPanel.prototype.getMiriamTypesDualListbox = function() {
+ return this._miriamTypesDualListbox;
+};
+
+ElementExportPanel.prototype.setIncludedCompartmentsDualListbox = function(dualListbox) {
+ this._includedCompartmentsDualListbox = dualListbox;
+};
+ElementExportPanel.prototype.getIncludedCompartmentsDualListbox = function() {
+ return this._includedCompartmentsDualListbox;
+};
+
+ElementExportPanel.prototype.getSelectedIncludedCompartments = function() {
+ var self = this;
+ var list = self.getIncludedCompartmentsDualListbox().selected;
+ var names = [];
+ var result = [];
+ for (var i = 0; i < list.length; i++) {
+ var element = list[i];
+ names[element.dataset.id] = true;
+ }
+ return self._getAllCompartments().then(function(compartments) {
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ if (names[compartment.getName()]) {
+ result.push(compartment);
+ }
+ }
+ return result;
+ })
+};
+
+ElementExportPanel.prototype.setExcludedCompartmentsDualListbox = function(dualListbox) {
+ this._excludedCompartmentsDualListbox = dualListbox;
+};
+ElementExportPanel.prototype.getExcludedCompartmentsDualListbox = function() {
+ return this._excludedCompartmentsDualListbox;
+};
+
+ElementExportPanel.prototype.getSelectedExcludedCompartments = function() {
+ var self = this;
+ var list = self.getExcludedCompartmentsDualListbox().selected;
+ var names = [];
+ var result = [];
+ for (var i = 0; i < list.length; i++) {
+ var element = list[i];
+ names[element.dataset.id] = true;
+ }
+ return self._getAllCompartments().then(function(compartments) {
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ if (names[compartment.getName()]) {
+ result.push(compartment);
+ }
+ }
+ return result;
+ })
+};
+
+ElementExportPanel.prototype.getSelectedMiriamTypes = function() {
+ var self = this;
+ return ServerConnector.getConfiguration().then(function(configuration) {
+ var selected = self.getMiriamTypesDualListbox().selected;
+ var result = [];
+ for (var i = 0; i < selected.length; i++) {
+ var miriamType = configuration.getMiriamTypeByName(selected[i].dataset.id);
+ result.push(miriamType);
+ }
+ return result;
+ });
+};
+
+ElementExportPanel.prototype.getSelectedColumns = function() {
+ var self = this;
+
+ var div = $("div[name='columnSelectDiv']", $(self.getElement()))[0];
+ var selectedColumnMap = [];
+ var selectedAll = false
+ $(":checked", $(div)).each(function(index, element) {
+ if (element.value === "ALL") {
+ selectedAll = true;
+ }
+ selectedColumnMap[element.value] = true;
+ });
+ var columnTypes = self.getAllColumns();
+
+ if (selectedAll) {
+ return Promise.resolve(columnTypes);
+ }
+
+ var result = [];
+
+ for (var i = 0; i < columnTypes.length; i++) {
+ var columnType = columnTypes[i];
+ if (selectedColumnMap[columnType.columnName] === true) {
+ result.push(columnType);
+ }
+ }
+ return Promise.resolve(result);
+}
+
+module.exports = ElementExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
new file mode 100644
index 0000000000000000000000000000000000000000..f11716e9f885907b0a61e4a4ccb121dc5d954d05
--- /dev/null
+++ b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
@@ -0,0 +1,26 @@
+"use strict";
+
+/* exported logger */
+
+var Panel = require('../Panel');
+
+var GuiConnector = require('../../GuiConnector');
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+function GraphicsExportPanel(params) {
+ params.panelName = "elementExport";
+ params.scrollable = true;
+ Panel.call(this, params);
+
+ var self = this;
+
+}
+
+GraphicsExportPanel.prototype = Object.create(Panel.prototype);
+GraphicsExportPanel.prototype.constructor = GraphicsExportPanel;
+
+GraphicsExportPanel.prototype.init = function() {
+
+}
+module.exports = GraphicsExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
new file mode 100644
index 0000000000000000000000000000000000000000..723980197e1217da6bf3accb3f516980ba2c4208
--- /dev/null
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -0,0 +1,27 @@
+"use strict";
+
+/* exported logger */
+
+var Panel = require('../Panel');
+
+var GuiConnector = require('../../GuiConnector');
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+function NetworkExportPanel(params) {
+ params.panelName = "elementExport";
+ params.scrollable = true;
+ Panel.call(this, params);
+
+ var self = this;
+
+}
+
+NetworkExportPanel.prototype = Object.create(Panel.prototype);
+NetworkExportPanel.prototype.constructor = NetworkExportPanel;
+
+NetworkExportPanel.prototype.init = function() {
+
+}
+
+module.exports = NetworkExportPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
index 15ac333fc566ad5c5e20a0aa361876ede2ae3647..c37a57bb6fddb6f9f0afbb400a3c523bc790ffa6 100644
--- a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
@@ -4,7 +4,7 @@
var Promise = require("bluebird");
-var Panel = require('./Panel');
+var Panel = require('../Panel');
var PanelControlElementType = require('../PanelControlElementType');
var logger = require('../../logger');
diff --git a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
index 8d8132e22ae32467adec07a9891ed06e83f848e7..2e13fa4bf64604f1851237af9b0617da9a624aaa 100644
--- a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
@@ -145,7 +145,7 @@ LeftPanel.prototype.init = function() {
return self.showElementDetails(e.arg.identifiedElements[0][0]);
} else {
return self.showElementDetails(undefined);
- }
+ }
});
resolve();
});
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 7ae652a0d74d756f0af0ac6760fa7efc4ed5027d..8da84fb8a91ff2ed3499b97ef329c03c2c6111b0 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -2,7 +2,7 @@
/* exported logger */
-var Panel = require('./Panel');
+var Panel = require('../Panel');
var PanelControlElementType = require('../PanelControlElementType');
var GuiConnector = require('../../GuiConnector');
diff --git a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
index 87b8616e0283cd559bb75807d39ac94ba139f598..79ba6d65c87e6cae67c9ccf7b5d459cde775bbcb 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
@@ -3,7 +3,7 @@
/* exported logger */
var ConfigurationType = require('../../ConfigurationType');
-var Panel = require('./Panel');
+var Panel = require('../Panel');
var PanelControlElementType = require('../PanelControlElementType');
var PublicationListDialog = require('./PublicationListDialog');
diff --git a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
index 8b261043578360cdaba4f63889567f992f1e062f..c7b819b0d220692f9d32ba37663ee230b659e7c6 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
@@ -4,7 +4,7 @@ var Promise = require("bluebird");
/* exported logger */
-var Panel = require('./Panel');
+var Panel = require('../Panel');
var PanelControlElementType = require('../PanelControlElementType');
var logger = require('../../logger');
diff --git a/frontend-js/src/main/js/map/data/Alias.js b/frontend-js/src/main/js/map/data/Alias.js
index fd27c126308cde818a123217b4d2819136e7ee84..a13785067d74eeac59d6bd53d544a883aa56608e 100644
--- a/frontend-js/src/main/js/map/data/Alias.js
+++ b/frontend-js/src/main/js/map/data/Alias.js
@@ -50,6 +50,7 @@ Alias.prototype.update = function(javaObject) {
return;
}
this.setDescription(javaObject.getDescription());
+ this.setElementId(javaObject.getElementId());
this.setType(javaObject.getType());
this.setCharge(javaObject.getCharge());
this.setSymbol(javaObject.getSymbol());
@@ -71,6 +72,7 @@ Alias.prototype.update = function(javaObject) {
return;
}
this.setDescription(javaObject.notes);
+ this.setElementId(javaObject.elementId);
this.setType(javaObject.type);
this.setCharge(javaObject.charge);
this.setSymbol(javaObject.symbol);
@@ -122,6 +124,14 @@ Alias.prototype.getY = function() {
return this.y;
};
+Alias.prototype.setElementId = function(elementId) {
+ this._elementId = elementId;
+};
+
+Alias.prototype.getElementId = function() {
+ return this._elementId;
+};
+
Alias.prototype.setWidth = function(width) {
this.width = width;
};
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 7f2633fd1b825bcb7fff41c9f0bfc582f39ab917..1906f20879297f0661d9f01b2a979cdf25abe324 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -5,6 +5,7 @@ var Promise = require("bluebird");
var logger = require('../../logger');
var Alias = require('./Alias');
+var IdentifiedElement = require('./IdentifiedElement');
var LayoutData = require('./LayoutData');
var PointData = require('./PointData');
var Reaction = require('./Reaction');
@@ -101,14 +102,20 @@ MapModel.prototype.getLayouts = function() {
/**
* Return list of all aliases that were added to the model.
*/
-MapModel.prototype.getAliases = function() {
- var result = [];
- for ( var id in this._aliases) {
- if (this._aliases.hasOwnProperty(id)) {
- result.push(this._aliases[id]);
+MapModel.prototype.getAliases = function(params) {
+ var self = this;
+ return ServerConnector.getAliases({
+ columns : "id,bounds,modelId",
+ type : params.type,
+ modelId : self.getId(),
+ }).then(function(lightAliases){
+ var identifiedElements = [];
+ for (var i=0;i<lightAliases.length;i++) {
+ self.addAlias(lightAliases[i]);
+ identifiedElements.push(new IdentifiedElement(lightAliases[i]));
}
- }
- return result;
+ return self.getByIdentifiedElements(identifiedElements, params.complete);
+ });
};
/**
@@ -139,7 +146,9 @@ MapModel.prototype.getCompleteAliasById = function(id) {
if (self._aliases[id] !== undefined && self._aliases[id].isComplete()) {
return Promise.resolve(self._aliases[id]);
} else {
- return ServerConnector.getAliases([ id ]).then(function(aliases) {
+ return ServerConnector.getAliases({
+ ids : id
+ }).then(function(aliases) {
if (self._aliases[id] === undefined) {
self._aliases[id] = aliases[0];
} else {
@@ -289,9 +298,14 @@ MapModel.prototype.getMissingElements = function(elements) {
var aliasPromise = null;
if (aliasIds.length > 0) {
if (elements.complete) {
- aliasPromise = ServerConnector.getAliases(aliasIds);
+ aliasPromise = ServerConnector.getAliases({
+ ids : aliasIds
+ });
} else {
- aliasPromise = ServerConnector.getLightAliases(aliasIds);
+ aliasPromise = ServerConnector.getAliases({
+ ids : aliasIds,
+ columns : "id,bounds,modelId"
+ });
}
}
@@ -475,11 +489,11 @@ MapModel.prototype.setMinZoom = function(minZoom) {
this._minZoom = minZoom;
};
-MapModel.prototype.getSubmodelType= function() {
+MapModel.prototype.getSubmodelType = function() {
return this._submodelType;
};
-MapModel.prototype.setSubmodelType= function(submodelType) {
+MapModel.prototype.setSubmodelType = function(submodelType) {
this._submodelType = submodelType;
};
@@ -729,4 +743,25 @@ MapModel.prototype.getReactionsForElements = function(elements, complete) {
});
};
+MapModel.prototype.getCompartments = function() {
+ var self = this;
+
+ var promise = Promise.resolve();
+ if (self._compartments === undefined) {
+ promise = ServerConnector.getAliases({
+ columns : "id,bounds,modelId",
+ type : "Compartment",
+ modelId : self.getId(),
+ }).then(function(compartments) {
+ self._compartments = [];
+ for (var i = 0; i < compartments.length; i++) {
+ self._compartments.push(new IdentifiedElement(compartments[i]));
+ }
+ });
+ }
+ return promise.then(function() {
+ return self.getByIdentifiedElements(self._compartments, true);
+ });
+};
+
module.exports = MapModel;
diff --git a/frontend-js/src/main/js/map/data/MiriamType.js b/frontend-js/src/main/js/map/data/MiriamType.js
new file mode 100644
index 0000000000000000000000000000000000000000..57b7387244aaadd90aeef121fad18de1f763dd96
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/MiriamType.js
@@ -0,0 +1,60 @@
+"use strict";
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+function MiriamType(data, name) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var self = this;
+ self.setUris(data.uris);
+ self.setHomepage(data.homepage);
+ self.setName(name);
+ self.setCommonName(data.commonName);
+ self.setRegistryIdentifier(data.registryIdentifier);
+}
+
+MiriamType.prototype = Object.create(ObjectWithListeners.prototype);
+MiriamType.prototype.constructor = MiriamType;
+
+MiriamType.prototype.setUris = function(uris) {
+ this._uris = uris;
+};
+
+MiriamType.prototype.getUris = function() {
+ return this._uris;
+};
+
+MiriamType.prototype.setHomepage = function(homepage) {
+ this._homepage = homepage;
+};
+
+MiriamType.prototype.getHomepage = function() {
+ return this._homepage;
+};
+
+MiriamType.prototype.setName = function(name) {
+ this._name = name;
+};
+
+MiriamType.prototype.getName = function() {
+ return this._name;
+};
+
+MiriamType.prototype.setCommonName = function(commonName) {
+ this._commonName = commonName;
+};
+
+MiriamType.prototype.getCommonName = function() {
+ return this._commonName;
+};
+
+MiriamType.prototype.setRegistryIdentifier = function(registryIdentifier) {
+ this._registryIdentifier = registryIdentifier;
+};
+
+MiriamType.prototype.getRegistryIdentifier = function() {
+ return this._registryIdentifier;
+};
+
+module.exports = MiriamType;
diff --git a/frontend-js/src/main/js/map/data/ProjectStatistics.js b/frontend-js/src/main/js/map/data/ProjectStatistics.js
new file mode 100644
index 0000000000000000000000000000000000000000..53e10ae5a5c8e1d172be63df88456e26572018f6
--- /dev/null
+++ b/frontend-js/src/main/js/map/data/ProjectStatistics.js
@@ -0,0 +1,50 @@
+"use strict";
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+var logger = require('../../logger');
+
+function ProjectStatistics(data, configuration) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ this.setReactionAnnotations(data.reactionAnnotations, configuration);
+ this.setElementAnnotations(data.elementAnnotations, configuration);
+}
+
+ProjectStatistics.prototype = Object.create(ObjectWithListeners.prototype);
+ProjectStatistics.prototype.constructor = ProjectStatistics;
+
+ProjectStatistics.prototype.setReactionAnnotations = function(reactionAnnotations, configuration) {
+ var self = this;
+ self._reactionAnnotations = [];
+ for ( var key in reactionAnnotations) {
+ if (reactionAnnotations.hasOwnProperty(key)) {
+ var miriamType = configuration.getMiriamTypeByName(key);
+ self._reactionAnnotations.push({
+ miriamType : miriamType,
+ count : reactionAnnotations[key]
+ });
+ }
+ }
+};
+
+ProjectStatistics.prototype.setElementAnnotations = function(elementAnnotations, configuration) {
+ var self = this;
+ self._elementAnnotations = [];
+ for ( var key in elementAnnotations) {
+ if (elementAnnotations.hasOwnProperty(key)) {
+ var miriamType = configuration.getMiriamTypeByName(key);
+ self._elementAnnotations.push({
+ miriamType : miriamType,
+ count : elementAnnotations[key]
+ });
+ }
+ }
+};
+
+ProjectStatistics.prototype.getElementAnnotations = function() {
+ return this._elementAnnotations;
+};
+
+module.exports = ProjectStatistics;
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 89cd1af7af67fbda743275c638a5e46e1aa4411e..f277b51de57127eb9fea2e50897b6e764902101d 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -9,6 +9,7 @@ var DbOverlayCollection = require('./map/overlay/DbOverlayCollection');
var ConfigurationType = require('./ConfigurationType');
var CustomMap = require('./map/CustomMap');
var CustomMapOptions = require('./map/CustomMapOptions');
+var Export = require('./Export');
var SearchDbOverlay = require('./map/overlay/SearchDbOverlay');
var LeftPanel = require('./gui/leftPanel/LeftPanel');
@@ -556,10 +557,35 @@ function create(params) {
}
+function createExport(params) {
+ params = modifyParamsForTouchInterface(params);
+ if (!(params instanceof CustomMapOptions)) {
+ params = new CustomMapOptions(params);
+ }
+ initGlobals(params);
+ params.getElement().style.display = "table";
+ params.getElement().innerHTML = "<div style='vertical-align:middle;display:table-cell;text-align: center'>"
+ + "<img src='resources/images/icons/ajax-loader.gif'/>" + "</div>";
+
+ var result;
+ // make sure that we are logged in
+ return ServerConnector.getToken().then(function() {
+ return getProject(params);
+ }).then(function(project) {
+ params.setProject(project);
+ result = new Export(params);
+ return result.init();
+ }).then(function() {
+ return result;
+ });
+}
+
var minerva = {
create : create,
+ createExport : createExport,
ServerConnector : OriginalServerConnector,
GuiConnector : OriginalGuiConnector,
+ DualListbox : require('dual-listbox').DualListbox,
};
module.exports = minerva;
diff --git a/frontend-js/src/test/js/Export-test.js b/frontend-js/src/test/js/Export-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..0a63026bd57d466136ec89de99bf5d90d8d9dce4
--- /dev/null
+++ b/frontend-js/src/test/js/Export-test.js
@@ -0,0 +1,28 @@
+"use strict";
+
+var Export = require('../../main/js/Export');
+var logger = require('./logger');
+
+var assert = require('assert');
+
+var originalNavigator = null;
+describe('Export', function() {
+
+ describe('init', function() {
+ it('default behaviour', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new Export({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+
+ });
+ });
+ });
+
+});
diff --git a/frontend-js/src/test/js/ServerConnector-test.js b/frontend-js/src/test/js/ServerConnector-test.js
index 7093188f2bc75d046c4bee2d07bbc04bac978cef..cb575f3384c06e952ffdc550afeecff86a8a2011 100644
--- a/frontend-js/src/test/js/ServerConnector-test.js
+++ b/frontend-js/src/test/js/ServerConnector-test.js
@@ -66,12 +66,11 @@ describe('ServerConnector', function() {
});
it('getElements with empty list of ids', function() {
- return ServerConnector.getLightAliases([]).then(function(result) {
- assert.equal(result.length, 2);
- var reaction = result[0];
- assert.ok(reaction instanceof Alias);
- assert.equal(reaction.getId(), 329176);
- assert.equal(reaction.getModelId(), 15781);
+ return ServerConnector.getAliases({}).then(function(result) {
+ assert.equal(result.length, 30);
+ var alias = result[0];
+ assert.ok(alias instanceof Alias);
+ assert.equal(alias.getModelId(), 15781);
});
});
diff --git a/frontend-js/src/test/js/gui/leftPanel/Panel-test.js b/frontend-js/src/test/js/gui/Panel-test.js
similarity index 73%
rename from frontend-js/src/test/js/gui/leftPanel/Panel-test.js
rename to frontend-js/src/test/js/gui/Panel-test.js
index 88d3dd98fd626b96e8fc870e6337a847130f0f98..f1d8211feb384b3056a92480cd74e059da2f351a 100644
--- a/frontend-js/src/test/js/gui/leftPanel/Panel-test.js
+++ b/frontend-js/src/test/js/gui/Panel-test.js
@@ -2,15 +2,15 @@
/* exported logger */
-var Helper = require('../../helper');
+var Helper = require('../helper');
-require('../../mocha-config.js');
+require('../mocha-config.js');
-var Panel = require('../../../../main/js/gui/leftPanel/Panel');
+var Panel = require('../../../main/js/gui/Panel');
var chai = require('chai');
var assert = chai.assert;
-var logger = require('../../logger');
+var logger = require('../logger');
describe('Panel', function() {
diff --git a/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..5805bf9d56b19cc3df800a23a398738545ad82fb
--- /dev/null
+++ b/frontend-js/src/test/js/gui/export/ElementExportPanel-test.js
@@ -0,0 +1,210 @@
+"use strict";
+
+var ElementExportPanel = require('../../../../main/js/gui/export/ElementExportPanel');
+var MiriamType = require('../../../../main/js/map/data/MiriamType');
+var logger = require('../../logger');
+
+var Helper = require('../../Helper');
+
+var assert = require('assert');
+
+describe('ElementExportPanel', function() {
+
+ var helper;
+ before(function() {
+ helper = new Helper();
+ });
+
+ describe('getSelectedTypes', function() {
+ it('select single element', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='Degraded']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ return exportObject.getSelectedTypes();
+ }).then(function(selectedTypes) {
+ assert.deepEqual([ "Degraded" ], selectedTypes);
+ });
+ });
+ it('select all', function() {
+ var exportObject;
+ var project;
+ var elementTypes;
+
+ return ServerConnector.getConfiguration().then(function(configuration) {
+ elementTypes = configuration.getElementTypes();
+ return ServerConnector.getProject();
+ }).then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='Degraded']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ $("input[name='ALL']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ return exportObject.getSelectedTypes();
+ }).then(function(selectedTypes) {
+ assert.deepEqual(elementTypes, selectedTypes);
+ });
+ });
+ });
+
+ describe('getSelectedColumns', function() {
+ it('select single element', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='column_name']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ return exportObject.getSelectedColumns();
+ }).then(function(selectedTypes) {
+ assert.equal([ "name" ], selectedTypes[0].columnName);
+ });
+ });
+ it('select all', function() {
+ var exportObject;
+ var project;
+ var elementTypes;
+
+ return ServerConnector.getConfiguration().then(function(configuration) {
+ elementTypes = configuration.getElementTypes();
+ return ServerConnector.getProject();
+ }).then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='column_name']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ $("input[name='ALL']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ return exportObject.getSelectedColumns();
+ }).then(function(selectedTypes) {
+ assert.equal(exportObject.getAllColumns().length, selectedTypes.length);
+ });
+ });
+ });
+
+ describe('getSelectedMiriamTypes', function() {
+ it('select single element', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ var dlb = exportObject.getMiriamTypesDualListbox();
+ var listItem = dlb.available[0];
+ dlb.addSelected(listItem);
+ return exportObject.getSelectedMiriamTypes();
+ }).then(function(result) {
+ assert.equal(result.length, 1);
+ assert.ok(result[0] instanceof MiriamType);
+ });
+ });
+ });
+
+ describe('getSelectedIncludedCompartments', function() {
+ it('empty selection', function() {
+ helper.setUrl("http://test/?id=complex_model_with_submaps");
+
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ assert.ok(exportObject.getIncludedCompartmentsDualListbox().available.length > 0);
+ return exportObject.getSelectedIncludedCompartments();
+ }).then(function(result) {
+ assert.equal(result.length, 0);
+ });
+ });
+ });
+
+ describe('getSelectedExcludedCompartments', function() {
+ it('empty selection', function() {
+ helper.setUrl("http://test/?id=complex_model_with_submaps");
+
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ var dlb = exportObject.getExcludedCompartmentsDualListbox();
+ var listItem = dlb.available[0];
+ dlb.addSelected(listItem);
+ return exportObject.getSelectedExcludedCompartments();
+ }).then(function(result) {
+ assert.equal(result.length, 1);
+ });
+ });
+ });
+
+ describe('createResponseString', function() {
+ it('get all', function() {
+ var exportObject;
+ var project;
+ return ServerConnector.getProject().then(function(result) {
+ project = result;
+ exportObject = new ElementExportPanel({
+ element : testDiv,
+ project : project
+ });
+ return exportObject.init();
+ }).then(function() {
+ $("input[name='ALL']", $(testDiv)).each(function(index, element) {
+ element.checked = true;
+ });
+ return exportObject.createResponseString();
+ }).then(function(result) {
+ // protein id
+ logger.debug (result)
+ assert.equal(result.indexOf("[object Object]"), -1);
+ assert.ok(result.indexOf("329156") >= 0);
+ });
+ });
+ });
+
+});
diff --git a/frontend-js/src/test/js/helper.js b/frontend-js/src/test/js/helper.js
index cf10fe386f3580d6899f5d9941a4d8056d68e220..539ad29dbf954598b09d3cccb9a714d54e43dc6b 100644
--- a/frontend-js/src/test/js/helper.js
+++ b/frontend-js/src/test/js/helper.js
@@ -27,6 +27,8 @@ var User = require("../../main/js/map/data/User");
var Cookies = require('js-cookie');
var jsdom = require('jsdom');
+var GuiConnector = require('../../main/js/GuiConnector');
+
function Helper() {
this.idCounter = 1000000;
}
@@ -355,10 +357,11 @@ Helper.prototype.createCustomMap = function(project) {
*/
Helper.prototype.setUrl = function(url) {
var cookies = Cookies.get();
- jsdom.changeURL(window, url);
+ dom.reconfigure({ url: url });
for ( var cookie in cookies) {
Cookies.set(cookie, cookies[cookie]);
}
+ GuiConnector.init();
};
Helper.EPSILON = 1e-6;
diff --git a/frontend-js/src/test/js/map/data/MapModel-test.js b/frontend-js/src/test/js/map/data/MapModel-test.js
index 64d9fd6b8d03f55d884ec5da35fdaabb08220f75..92682f85555996d2629b88d5088efb9f2c6c697a 100644
--- a/frontend-js/src/test/js/map/data/MapModel-test.js
+++ b/frontend-js/src/test/js/map/data/MapModel-test.js
@@ -23,9 +23,8 @@ describe('MapModel', function() {
idObject : 123
});
- assert.equal(123, model.id);
+ assert.equal(123, model.getId());
- assert.ok(model.getAliases());
assert.ok(model.getLayoutsData());
});
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index 253c6bebd7eb54d647b457649553c30c1f0a7a00..c6707b206f3c59147110ef4d647032bb733e7bc8 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -490,4 +490,16 @@ describe('minerva global', function() {
});
+ it('create Export', function() {
+ var options = null;
+ return ServerConnectorMock.getProject().then(function(project) {
+ options = helper.createCustomMapOptions(project);
+
+ return minerva.createExport(options);
+ }).then(function(result) {
+ assert.ok(result);
+ assert.equal(logger.getWarnings().length, 0);
+ });
+ });
+
});
diff --git a/frontend-js/src/test/js/mocha-config.js b/frontend-js/src/test/js/mocha-config.js
index 823dfc3ef0c133745daec8488016a6561d25dde0..db423ba524b9944c97eaf67a6aaab6fa9f2358f5 100644
--- a/frontend-js/src/test/js/mocha-config.js
+++ b/frontend-js/src/test/js/mocha-config.js
@@ -14,8 +14,9 @@ global.navigator = {
};
var jsdom = require('jsdom');
-global.document = jsdom.jsdom(undefined);
-global.window = document.defaultView;
+global.dom = new jsdom.JSDOM();
+global.window = dom.window;
+global.document = window.document;
global.$ = require('jQuery');
global.jQuery = $;
@@ -23,6 +24,17 @@ global.window.$ = $;
// additions to jsdom implementations:
global.Option = window.Option;
+
+var originalCreateElement = document.createElement;
+document.createElement = function(arg) {
+ var result = originalCreateElement.call(this, arg);
+ //woraround for: https://github.com/tmpvar/jsdom/issues/961
+ if ("li" === arg) {
+ result.dataset = [];
+ }
+ return result;
+};
+
window.open = function() {
var result = {};
result.focus = function() {
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index 309b4b885947a49b6453a7d9cf1f0574f33a0950..328a5df52c4c125d31c1ed89541791af3fc0c772 100644
--- a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","name":"SBGN-ML"}],"elementTypes":["Drug","Degraded","Phenotype","Gene","RNA","Unknown","Compartment","Antisense RNA","Ion","Simple molecule","Protein","Complex"],"imageFormats":[{"handler":"lcsb.mapviewer.converter.graphics.PngImageGenerator","name":"PNG image"},{"handler":"lcsb.mapviewer.converter.graphics.PdfImageGenerator","name":"PDF"}],"options":[{"idObject":9,"type":"EMAIL_ADDRESS","value":"your.account@domain.com"},{"idObject":10,"type":"EMAIL_LOGIN","value":"your@login"},{"idObject":11,"type":"EMAIL_PASSWORD","value":"email.secret.password"},{"idObject":13,"type":"EMAIL_IMAP_SERVER","value":"your.imap.domain.com"},{"idObject":12,"type":"EMAIL_SMTP_SERVER","value":"your.smtp.domain.com"},{"idObject":14,"type":"EMAIL_SMTP_PORT","value":"25"},{"idObject":6,"type":"DEFAULT_MAP","value":"sample"},{"idObject":4,"type":"LOGO_IMG","value":"udl.png"},{"idObject":3,"type":"LOGO_LINK","value":"http://wwwen.uni.lu/"},{"idObject":7,"type":"SEARCH_DISTANCE","value":"10"},{"idObject":1,"type":"REQUEST_ACCOUNT_EMAIL","value":"your.email@domain.com"},{"idObject":8,"type":"SEARCH_RESULT_NUMBER","value":"100"},{"idObject":2,"type":"GOOGLE_ANALYTICS_IDENTIFIER","value":""},{"idObject":5,"type":"LOGO_TEXT","value":"University of Luxembourg"},{"idObject":56,"type":"X_FRAME_DOMAIN","value":"http://localhost:8080/"},{"idObject":131,"type":"BIG_FILE_STORAGE_DIR","value":"minerva-big/"},{"idObject":138,"type":"LENGEND_FILE_1","value":"resources/images/legend_a.png"},{"idObject":139,"type":"LENGEND_FILE_2","value":"resources/images/legend_b.png"},{"idObject":140,"type":"LENGEND_FILE_3","value":"resources/images/legend_c.png"},{"idObject":141,"type":"LENGEND_FILE_4","value":"resources/images/legend_d.png"},{"idObject":142,"type":"USER_MANUAL_FILE","value":"resources/other/user_guide.pdf"},{"idObject":205,"type":"MIN_COLOR_VAL","value":"FF0000"},{"idObject":206,"type":"MAX_COLOR_VAL","value":"fbff00"}],"overlayTypes":[{"name":"GENERIC"},{"name":"GENETIC_VARIANT"}],"reactionTypes":["Unknown reduced modulation","Reduced physical stimulation","Translation","State transition","Transcription","Unknown reduced trigger","Negative influence","Unknown positive influence","Positive influence","Unknown transition","Truncation","Reduced trigger","Boolean logic gate","Unknown reduced physical stimulation","Generic Reaction","Heterodimer associaation","Reduced modulation","Unknown negative influence","Dissociation","Known transition omitted","Transport"]}
\ No newline at end of file
+{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","name":"SBGN-ML"}],"elementTypes":["Drug","Degraded","Phenotype","Gene","RNA","Unknown","Compartment","Antisense RNA","Ion","Simple molecule","Protein","Complex"],"miriamTypes":{"CHEMBL_TARGET":{"commonName":"ChEMBL target","uris":["urn:miriam:chembl.target"],"homepage":"https://www.ebi.ac.uk/chembldb/","registryIdentifier":"MIR:00000085"},"UNIPROT":{"commonName":"Uniprot","uris":["urn:miriam:uniprot"],"homepage":"http://www.uniprot.org/","registryIdentifier":"MIR:00000005"},"MI_R_BASE_MATURE_SEQUENCE":{"commonName":"miRBase Mature Sequence Database","uris":["urn:miriam:mirbase.mature"],"homepage":"http://www.mirbase.org/","registryIdentifier":"MIR:00000235"},"PFAM":{"commonName":"Protein Family Database","uris":["urn:miriam:pfam"],"homepage":"http://pfam.xfam.org//","registryIdentifier":"MIR:00000028"},"ENSEMBL_PLANTS":{"commonName":"Ensembl Plants","uris":["urn:miriam:ensembl.plant"],"homepage":"http://plants.ensembl.org/","registryIdentifier":"MIR:00000205"},"WIKIPEDIA":{"commonName":"Wikipedia (English)","uris":["urn:miriam:wikipedia.en"],"homepage":"http://en.wikipedia.org/wiki/Main_Page","registryIdentifier":"MIR:00000384"},"CHEBI":{"commonName":"Chebi","uris":["urn:miriam:obo.chebi","urn:miriam:chebi"],"homepage":"http://www.ebi.ac.uk/chebi/","registryIdentifier":"MIR:00000002"},"WIKIDATA":{"commonName":"Wikidata","uris":["urn:miriam:wikidata"],"homepage":"https://www.wikidata.org/","registryIdentifier":"MIR:00000549"},"REACTOME":{"commonName":"Reactome","uris":["urn:miriam:reactome"],"homepage":"http://www.reactome.org/","registryIdentifier":"MIR:00000018"},"EC":{"commonName":"Enzyme Nomenclature","uris":["urn:miriam:ec-code"],"homepage":"http://www.enzyme-database.org/","registryIdentifier":"MIR:00000004"},"UNIPROT_ISOFORM":{"commonName":"UniProt Isoform","uris":["urn:miriam:uniprot.isoform"],"homepage":"http://www.uniprot.org/","registryIdentifier":"MIR:00000388"},"OMIM":{"commonName":"Online Mendelian Inheritance in Man","uris":["urn:miriam:omim"],"homepage":"http://omim.org/","registryIdentifier":"MIR:00000016"},"DRUGBANK_TARGET_V4":{"commonName":"DrugBank Target v4","uris":["urn:miriam:drugbankv4.target"],"homepage":"http://www.drugbank.ca/targets","registryIdentifier":"MIR:00000528"},"MIR_TAR_BASE_MATURE_SEQUENCE":{"commonName":"miRTarBase Mature Sequence 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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Compartment&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/elements/columns=id,bounds,modelId&type=Compartment&token=MOCK_TOKEN_ID&
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diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/columns=id,bounds,modelId&token=MOCK_TOKEN_ID&
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molecule","abbreviation":null,"compartmentId":null,"name":"GTP","bounds":{"x":849.0,"width":70.0,"y":309.0,"height":25.0},"formula":null,"id":329180,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]},{"symbol":null,"formerSymbols":[],"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"s22","bounds":{"x":918.0,"width":80.0,"y":427.0,"height":40.0},"formula":null,"id":329162,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]},{"symbol":null,"formerSymbols":[],"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Simple molecule","abbreviation":null,"compartmentId":null,"name":"GDP","bounds":{"x":959.0,"width":70.0,"y":271.0,"height":25.0},"formula":null,"id":329156,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]},{"symbol":null,"formerSymbols":[],"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":329158,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"s14","bounds":{"x":279.0,"width":80.0,"y":233.0,"height":40.0},"formula":null,"id":329159,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]},{"symbol":null,"formerSymbols":[],"notes":"","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Phenotype","abbreviation":null,"compartmentId":null,"name":"s7","bounds":{"x":213.0,"width":80.0,"y":128.0,"height":30.0},"formula":null,"id":329172,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]},{"symbol":null,"formerSymbols":[],"notes":"description of S1\r\nthird line","references":[],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"s1","bounds":{"x":12.0,"width":80.0,"y":6.0,"height":40.0},"formula":null,"id":329173,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]},{"symbol":null,"formerSymbols":[],"notes":"","references":[{"resource":"622","link":"http://www.ncbi.nlm.nih.gov/gene/622","id":860352,"type":"ENTREZ"}],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"BDH1","bounds":{"x":1225.7682370820667,"width":80.0,"y":66.0,"height":40.0},"formula":null,"id":329170,"linkedSubmodel":null,"hierarchyVisibilityLevel":[]}]
\ No newline at end of file
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..929cc68f9c59295ea64afef542c1b3a3ef16caa7
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/statistics/token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"reactionAnnotations":{"SGD":0,"HGNC_SYMBOL":0,"GO":0,"MI_R_BASE_SEQUENCE":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"REACTOME":2,"ENSEMBL":0,"OMIM":0,"CHEBI":0,"KEGG_COMPOUND":0,"DRUGBANK":0,"UNIGENE":0,"KEGG_ORTHOLOGY":0,"CHEMBL_TARGET":0,"WORM_BASE":0,"ENSEMBL_PLANTS":0,"REFSEQ":0,"ENTREZ":0,"UNKNOWN":0,"MI_R_BASE_MATURE_SEQUENCE":0,"UNIPROT_ISOFORM":0,"COG":0,"TAXONOMY":0,"KEGG_REACTION":0,"TOXICOGENOMIC_CHEMICAL":0,"CHEMSPIDER":0,"TAIR_LOCUS":0,"UNIPROT":0,"PHARM":0,"CCDS":0,"HGNC":0,"WIKIPEDIA":0,"HMDB":0,"PANTHER":0,"WIKIDATA":0,"PUBCHEM_SUBSTANCE":0,"CAS":0,"KEGG_PATHWAY":0,"MGD":0,"PUBMED":1,"CHEMBL_COMPOUND":0,"PFAM":0,"MESH_2012":0,"EC":0,"PUBCHEM":0,"DRUGBANK_TARGET_V4":0,"WIKIPATHWAYS":0,"INTERPRO":0,"KEGG_GENES":0},"elementAnnotations":{"SGD":0,"HGNC_SYMBOL":0,"GO":0,"MI_R_BASE_SEQUENCE":0,"MIR_TAR_BASE_MATURE_SEQUENCE":0,"REACTOME":4,"ENSEMBL":0,"OMIM":0,"CHEBI":0,"KEGG_COMPOUND":0,"DRUGBANK":0,"UNIGENE":0,"KEGG_ORTHOLOGY":0,"CHEMBL_TARGET":0,"WORM_BASE":0,"ENSEMBL_PLANTS":0,"REFSEQ":5,"ENTREZ":2,"UNKNOWN":0,"MI_R_BASE_MATURE_SEQUENCE":0,"UNIPROT_ISOFORM":0,"COG":0,"TAXONOMY":0,"KEGG_REACTION":0,"TOXICOGENOMIC_CHEMICAL":0,"CHEMSPIDER":0,"TAIR_LOCUS":0,"UNIPROT":0,"PHARM":1,"CCDS":0,"HGNC":1,"WIKIPEDIA":0,"HMDB":0,"PANTHER":0,"WIKIDATA":0,"PUBCHEM_SUBSTANCE":0,"CAS":0,"KEGG_PATHWAY":0,"MGD":0,"PUBMED":0,"CHEMBL_COMPOUND":0,"PFAM":0,"MESH_2012":0,"EC":0,"PUBCHEM":0,"DRUGBANK_TARGET_V4":0,"WIKIPATHWAYS":0,"INTERPRO":0,"KEGG_GENES":1}}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index abe96fcaf95f5e1123465b45a38b8105386cccbe..200c6958ad5c838acdb07e09de5e8234ae014475 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
@@ -28,6 +28,7 @@ public class ConfigurationController extends BaseController {
result.put("overlayTypes", configurationController.getOverlayTypes(token));
result.put("elementTypes", configurationController.getElementTypes(token));
result.put("reactionTypes", configurationController.getReactionTypes(token));
+ result.put("miriamTypes", configurationController.getMiriamTypes(token));
return result;
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 8ce9ac5c13a0b268c57ec0f0b1a6c004aec3a075..30367df7cf9928650dbc0611a9812ac45c5917e8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -22,6 +22,7 @@ import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ClassTreeNode;
@@ -169,4 +170,22 @@ public class ConfigurationRestImpl {
return getClassStringTypesList(Reaction.class);
}
+ public Map<String, Object> getMiriamTypes(String id) {
+ Map<String, Object> result = new HashMap<>();
+ for (MiriamType type : MiriamType.values()) {
+ result.put(type.name(), createMiriamTypeResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createMiriamTypeResponse(MiriamType type) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("commonName", type.getCommonName());
+ result.put("homepage", type.getDbHomepage());
+ result.put("registryIdentifier", type.getRegistryIdentifier());
+ result.put("uris", type.getUris());
+
+ return result;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index a21b6e6164c5429eabd594ddeff02cb59c8c3210..ca0c72a1213ceb9a5309643f95ef843e61b1a0b2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -37,6 +37,14 @@ public class ProjectController extends BaseController {
return projectController.getMetaData(projectId, token);
}
+ @RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Object getStatistics(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getStatistics(projectId, token);
+ }
+
@RequestMapping(value = "/projects/{projectId}:downloadSource", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public ResponseEntity<byte[]> getProjectSource(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index a90edd7c34d3a31fbd94bfc0f0263a1fa2b5fb1d..cba3a43808693c1ebe96e3858c2a5b76aa157f2a 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -8,6 +8,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
@@ -41,6 +42,8 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewImageLink;
import lcsb.mapviewer.model.map.OverviewLink;
@@ -48,6 +51,8 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
@@ -388,4 +393,51 @@ public class ProjectRestImpl extends BaseRestImpl {
}
+ public Map<String, Object> getStatistics(String projectId, String token) throws SecurityException, ObjectNotFoundException {
+ Map<String, Object> result = new HashMap<String, Object>();
+ AuthenticationToken authenticationToken = userService.getToken(token);
+
+ Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ if (model == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Map<MiriamType, Integer> elementAnnotations = new HashMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ elementAnnotations.put(mt, 0);
+ }
+ Set<Model> models = new HashSet<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+
+ for (Model model2 : models) {
+ for (Element alias : model2.getElements()) {
+ for (MiriamData md : alias.getMiriamData()) {
+ Integer amount = elementAnnotations.get(md.getDataType());
+ amount += 1;
+ elementAnnotations.put(md.getDataType(), amount);
+ }
+ }
+ }
+ result.put("elementAnnotations", elementAnnotations);
+
+ Map<MiriamType, Integer> reactionAnnotations = new HashMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ reactionAnnotations.put(mt, 0);
+ }
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ Integer amount = reactionAnnotations.get(md.getDataType());
+ amount += 1;
+ reactionAnnotations.put(md.getDataType(), amount);
+ }
+ }
+ }
+
+ result.put("reactionAnnotations", reactionAnnotations);
+
+ return result;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
index 8fd5ac43cf5e07240c13d8ee38592f273dad1f00..21b5336199ad0f71bc68dd588c58abfa50d53081 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
@@ -27,10 +27,11 @@ public class ElementsController extends BaseController {
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "modelId") String modelId, //
@RequestParam(value = "id", defaultValue = "") String id, //
+ @RequestParam(value = "type", defaultValue = "") String type, //
@RequestParam(value = "columns", defaultValue = "") String columns, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token//
) throws SecurityException {
- return projectController.getElements(projectId, id, columns, modelId, token);
+ return projectController.getElements(projectId, id, columns, modelId, token, type);
}
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index d9ce7b914dbe1640c8cd8f14fd9b2f89a50e6d1f..087f49f4b5dc44ead6eebba48b8767b657f6d372 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -36,7 +36,7 @@ public class ElementsRestImpl extends BaseRestImpl {
@Autowired
private OverviewImageViewFactory factory;
- public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId, String token)
+ public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId, String token, String type)
throws UserAccessException, SecurityException {
Set<Integer> ids = new HashSet<>();
if (!id.equals("")) {
@@ -44,6 +44,13 @@ public class ElementsRestImpl extends BaseRestImpl {
ids.add(Integer.valueOf(str));
}
}
+ Set<String> types = new HashSet<>();
+ if (!type.isEmpty()) {
+ for (String str : type.split(",")) {
+ types.add(str.toLowerCase());
+ }
+ }
+
Set<String> columnsSet = createElementColumnSet(columns);
List<Map<String, Object>> result = new ArrayList<>();
@@ -53,7 +60,9 @@ public class ElementsRestImpl extends BaseRestImpl {
for (Model model2 : models) {
for (Element element : model2.getElements()) {
if (ids.size() == 0 || ids.contains(element.getId())) {
- result.add(preparedElement(element, columnsSet));
+ if (types.size() == 0 || types.contains(element.getStringType().toLowerCase())) {
+ result.add(preparedElement(element, columnsSet));
+ }
}
}
}
@@ -70,6 +79,8 @@ public class ElementsRestImpl extends BaseRestImpl {
value = element.getId();
} else if (column.equals("modelid")) {
value = element.getModelData().getId();
+ } else if (column.equals("elementid")) {
+ value = element.getElementId();
} else if (column.equals("name")) {
value = element.getName();
} else if (column.equals("type")) {
@@ -129,6 +140,7 @@ public class ElementsRestImpl extends BaseRestImpl {
Set<String> columnsSet = new HashSet<>();
if (columns.equals("")) {
columnsSet.add("id");
+ columnsSet.add("elementId");
columnsSet.add("modelId");
columnsSet.add("name");
columnsSet.add("type");
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
index c424749d187a2e9cf32f69cf86694aae3645580e..52b5c6aa884540de6efa5ed1602bf858750a62a2 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.api.configuration;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.util.List;
@@ -14,6 +15,7 @@ import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.services.view.ConfigurationView;
@@ -81,7 +83,6 @@ public class ConfigurationRestImplTest extends RestTestFunctions {
e.printStackTrace();
throw e;
}
-
}
@Test
@@ -94,7 +95,17 @@ public class ConfigurationRestImplTest extends RestTestFunctions {
e.printStackTrace();
throw e;
}
+ }
+ @Test
+ public void testGetMiriamTypes() throws Exception {
+ try {
+ Map<?,?> list = configurationRestImpl.getMiriamTypes(token.getId());
+ assertNotNull(list.get(MiriamType.PUBMED.name()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
}
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index d9d477bee8dd8c3ae0268530438385f4949bc122..12a789d393bd4674120a9568735b6ac54bae29e6 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -1,10 +1,13 @@
package lcsb.mapviewer.api.projects;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
+import java.util.Map;
+
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
@@ -21,6 +24,7 @@ import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
@@ -124,6 +128,28 @@ public class ProjectRestImplTest extends RestTestFunctions {
}
}
+ @Test
+ public void testGetStatistics() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getStatistics("sample", token.getId());
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+
+ Map<?, ?> elementAnnotations = (Map<?, ?>) result.get("elementAnnotations");
+ assertEquals(elementAnnotations.get(MiriamType.CAS), 0);
+ assertEquals(elementAnnotations.get(MiriamType.ENTREZ), 1);
+
+ Map<?, ?> reactionAnnotations = (Map<?, ?>) result.get("reactionAnnotations");
+ assertEquals(reactionAnnotations.get(MiriamType.ENTREZ), 0);
+ assertEquals(reactionAnnotations.get(MiriamType.PUBMED), 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testGetMetaDataForComplexWithImages() throws Exception {
try {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index f3c30757319e0f2098957d09eb3da05e0b809b58..8cc6d689ba44e9c600f646ff1290167135c709d9 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.api.projects.models.bioEntities.elements;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.mockito.Matchers.any;
@@ -8,6 +9,7 @@ import static org.mockito.Matchers.anyString;
import java.util.List;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
@@ -19,14 +21,16 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.services.interfaces.IModelService;
public class ElementRestImplTest extends RestTestFunctions {
+ Logger logger = Logger.getLogger(RestTestFunctions.class);
@Autowired
ElementsRestImpl _elementsRestImpl;
- ObjectMapper mapper = new ObjectMapper();
+ ObjectMapper mapper = new ObjectMapper();
@AfterClass
public static void tearDownAfterClass() throws Exception {
@@ -44,7 +48,7 @@ public class ElementRestImplTest extends RestTestFunctions {
public void testGetElementsProcessAllColumns() throws Exception {
try {
ElementsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId());
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "");
for (Map<String, Object> element : result) {
for (String paramName : element.keySet()) {
Object val = element.get(paramName);
@@ -57,7 +61,21 @@ public class ElementRestImplTest extends RestTestFunctions {
}
String json = mapper.writeValueAsString(result);
assertNotNull(json);
-
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetElementsByType() throws Exception {
+ try {
+ String proteinType = new GenericProtein("1").getStringType();
+ ElementsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType);
+ assertEquals(12, result.size());
+
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/web/.gitignore b/web/.gitignore
index 3a1f4b74967f5ce7841e10a963c327f921692a4b..b334afad6491840a0b5c204e1ea0b214baac12db 100644
--- a/web/.gitignore
+++ b/web/.gitignore
@@ -1,4 +1,5 @@
/node_modules/
/coverage/
+/src/main/webapp/resources/css/minerva.css
/src/main/webapp/resources/js/minerva.js
/src/main/webapp/resources/js/minerva.js.map
diff --git a/web/pom.xml b/web/pom.xml
index 8e1ec90cb6d4c87eea0c219ef90eee7128b79747..db2c44d95b4458d191c8bdb615e6e1a03a0c9c92 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -203,8 +203,7 @@
<version>2.7</version>
<executions>
<execution>
- <id>copy-resources</id>
- <!-- here the phase you need -->
+ <id>copy-js</id>
<phase>prepare-package</phase>
<goals>
<goal>copy-resources</goal>
@@ -222,6 +221,24 @@
</resources>
</configuration>
</execution>
+ <execution>
+ <id>copy-css</id>
+ <phase>prepare-package</phase>
+ <goals>
+ <goal>copy-resources</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${basedir}/src/main/webapp/resources/css/</outputDirectory>
+ <resources>
+ <resource>
+ <directory>${basedir}/../frontend-js/dist/</directory>
+ <includes>
+ <include>**/*.css</include>
+ </includes>
+ </resource>
+ </resources>
+ </configuration>
+ </execution>
</executions>
</plugin>
</plugins>
diff --git a/web/src/main/webapp/WEB-INF/components/admin/header.xhtml b/web/src/main/webapp/WEB-INF/components/admin/header.xhtml
index 7361ab78ee149d75a73cf319fc0b98a6bd62164e..3f4bf95ce2fd7a0df3814e6ac9ac802808ca0da0 100644
--- a/web/src/main/webapp/WEB-INF/components/admin/header.xhtml
+++ b/web/src/main/webapp/WEB-INF/components/admin/header.xhtml
@@ -4,7 +4,7 @@
xmlns:ui="http://java.sun.com/jsf/facelets"
xmlns:p="http://primefaces.org/ui">
- <h:outputStylesheet library="css" name="global.css" />
+ <h:outputStylesheet library="css" name="minerva.css" />
<div class="minerva-header">
<a href="#{request.contextPath}/?id=#{mapMB.currentMapId}" class="mainTitle"><i class="fa fa-home" style="font-size:17px"></i> #{mapMB.currentProject.name}</a>
diff --git a/web/src/main/webapp/export-new.xhtml b/web/src/main/webapp/export-new.xhtml
new file mode 100644
index 0000000000000000000000000000000000000000..e84a149b5e2969e49651600830450d5271be382b
--- /dev/null
+++ b/web/src/main/webapp/export-new.xhtml
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml"
+ xmlns:h="http://java.sun.com/jsf/html"
+ xmlns:f="http://java.sun.com/jsf/core"
+ xmlns:ui="http://java.sun.com/jsf/facelets"
+ xmlns:p="http://primefaces.org/ui">
+
+<f:view contentType="text/html">
+<h:head>
+ <script src="https://maps.google.com/maps/api/js?libraries=drawing&v=3.26" type="text/javascript"/>
+
+ <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" type="text/javascript"/>
+ <script src="https://twitter.github.io/typeahead.js/releases/latest/typeahead.bundle.min.js" type="text/javascript"/>
+
+ <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.js"></script>
+ <script src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
+
+
+ <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.13/css/jquery.dataTables.min.css"/>
+ <link rel="stylesheet" type="text/css" href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css"/>
+
+ <link rel="shortcut icon" href="./resources/images/favicon.png" type="image/png" />
+
+ <h:outputScript library="js" name="minerva.js" />
+
+ <script type="text/javascript">
+//<![CDATA[
+
+function initMap(){
+ var element = document.getElementById('minervaAppDiv');
+ return minerva.createExport({
+ element : element,
+ }).then(function(result){
+ customMap = result;
+ document.title = result.getProject().getName();
+ }).catch(function(rejectReason){
+ minerva.GuiConnector.alert(rejectReason);
+ });
+}
+
+//]]>
+ </script>
+</h:head>
+<h:body onload="initMap();" >
+<h:outputStylesheet library="css" name="style.css"/>
+<h:outputStylesheet library="css" name="minerva.css" />
+<h:outputStylesheet library="css" name="pileup.css"/>
+<h:outputStylesheet library="css" name="bootstrap.min.css"/>
+
+ <h:outputScript library="primefaces" name="jquery/jquery.js" target="head" />
+ <div id="minervaAppDiv" style="height: 100%;width: 100%;margin: 0;"/>
+
+</h:body>
+</f:view>
+</html>
diff --git a/web/src/main/webapp/index.xhtml b/web/src/main/webapp/index.xhtml
index ee5341d581deae5af4a8e02902ff9e71c5ceb1f2..f950f192d10f51a8dfaa31c11052bdc16080fdc7 100644
--- a/web/src/main/webapp/index.xhtml
+++ b/web/src/main/webapp/index.xhtml
@@ -48,7 +48,7 @@ function initMap(){
</h:head>
<h:body onload="initMap();" >
<h:outputStylesheet library="css" name="style.css"/>
-<h:outputStylesheet library="css" name="global.css" />
+<h:outputStylesheet library="css" name="minerva.css" />
<h:outputStylesheet library="css" name="pileup.css"/>
<h:outputStylesheet library="css" name="bootstrap.min.css"/>